Abstract : The ability to support Quality of Service (QoS) constraints is an important requirement in some scientific applications. With the increasing use of Cloud computing infrastructures, where access to resources is shared, dynamic and provisioned on-demand, identifying how QoS constraints can be supported becomes an important challenge. However, access to dedicated resources is often not possible in existing Cloud deployments and limited QoS guarantees are provided by many commercial providers (often restricted to error rate and availability, rather than particular QoS metrics such as latency or access tulle). We propose a workflow system architecture which enforces QoS for the simultaneous execution of multiple scientific workflows over a shared infrastructure (such as a Cloud environment). Our approach involves multiple pipeline workflow instances, with each instance having its own QoS requirements. These workflows are composed of a number of stages, with each stage being mapped to one or more physical resources. A stage involves a combination of data access, computation and data transfer capability. A token bucket-based data throttling framework is embedded into the workflow system architecture. Each workflow instance stage regulates the amount of data that is injected into the shared resources, allowing for bursts of data to be injected while at the same time providing isolation of workflow streams. We demonstrate our approach by using the Montage workflow, and develop a Reference net model of the workflow. (C) 2011 Elsevier Inc. All rights reserved.